Modulome

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.9

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Modulome
        Analysis of public microbial RNA-seq data

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Contact E-mail
        avsastry@ucsd.edu
        Application Type
        Microbial RNA-seq Analysis

        Report generated on 2022-02-15, 00:41 based on data in: /home/saugat/Dropbox (UCSD SBRG)/Desktop/modulome-nextflow/aws_results


        General Statistics

        Showing 386/386 rows and 9/10 columns.
        Sample Name% AssignedM Assigned% AlignedM Aligned% BP Trimmed% Dups% GCLengthM Seqs
        CM_1
        82.2%
        9.6
        98.2%
        11.4
        1.1%
        85.5%
        35%
        39 bp
        11.6
        CM_10
        80.7%
        9.7
        98.0%
        11.8
        1.1%
        86.3%
        37%
        39 bp
        12.1
        CM_11
        81.0%
        9.1
        98.1%
        11.1
        1.6%
        85.0%
        37%
        39 bp
        11.3
        CM_12
        81.5%
        9.1
        98.0%
        11.0
        1.1%
        84.8%
        37%
        39 bp
        11.2
        CM_13
        85.8%
        9.2
        98.0%
        10.5
        1.1%
        83.7%
        35%
        39 bp
        10.8
        CM_14
        85.6%
        9.4
        97.9%
        10.8
        1.1%
        83.8%
        35%
        40 bp
        11.0
        CM_15
        86.0%
        9.3
        98.2%
        10.6
        1.1%
        84.6%
        36%
        40 bp
        10.8
        CM_16
        84.6%
        9.9
        98.1%
        11.5
        1.1%
        85.1%
        36%
        39 bp
        11.7
        CM_2
        83.6%
        7.9
        98.1%
        9.2
        1.0%
        83.4%
        34%
        39 bp
        9.4
        CM_3
        79.1%
        7.4
        98.1%
        9.2
        1.0%
        83.9%
        36%
        40 bp
        9.4
        CM_4
        83.8%
        8.0
        98.2%
        9.4
        1.0%
        83.6%
        35%
        39 bp
        9.5
        CM_5
        80.5%
        9.1
        97.9%
        11.1
        1.1%
        84.6%
        36%
        39 bp
        11.3
        CM_6
        83.6%
        9.6
        98.0%
        11.3
        1.7%
        84.6%
        35%
        39 bp
        11.5
        CM_7
        84.3%
        10.1
        97.9%
        11.8
        1.1%
        84.5%
        35%
        40 bp
        12.0
        CM_8
        85.1%
        9.4
        98.0%
        10.8
        1.7%
        84.0%
        34%
        39 bp
        11.1
        CM_9
        84.2%
        10.7
        97.9%
        12.5
        1.7%
        85.6%
        36%
        40 bp
        12.7
        Cody_1
        70.8%
        2.4
        79.8%
        2.7
        0.4%
        72.0%
        35%
        151 bp
        3.4
        Cody_2
        70.5%
        3.6
        79.2%
        4.0
        0.6%
        75.6%
        35%
        151 bp
        5.1
        Cody_3
        73.6%
        7.5
        95.3%
        9.7
        0.9%
        82.0%
        35%
        50 bp
        10.2
        Cody_4
        75.3%
        8.2
        97.1%
        10.6
        1.3%
        84.7%
        35%
        51 bp
        10.9
        ERX4294041
        74.0%
        5.1
        0.0%
        85.2%
        34%
        70 bp
        6.9
        ERX4294042
        74.1%
        6.4
        0.0%
        84.4%
        34%
        70 bp
        8.6
        ERX4294043
        75.1%
        6.7
        0.0%
        84.0%
        34%
        70 bp
        8.9
        ERX4294044
        80.2%
        5.8
        0.0%
        82.8%
        34%
        70 bp
        7.3
        ERX4294045
        79.8%
        5.9
        0.2%
        82.7%
        35%
        70 bp
        7.4
        ERX4294046
        79.3%
        6.2
        0.0%
        82.2%
        34%
        70 bp
        7.8
        ERX4294047
        77.8%
        5.9
        0.2%
        84.9%
        34%
        70 bp
        7.6
        ERX4294048
        74.8%
        5.3
        0.6%
        84.4%
        35%
        70 bp
        7.1
        ERX4294049
        77.1%
        6.1
        0.0%
        85.3%
        35%
        70 bp
        7.9
        ERX4294050
        77.5%
        5.5
        0.3%
        84.8%
        35%
        70 bp
        7.1
        ERX4294051
        79.8%
        6.5
        0.0%
        83.2%
        34%
        70 bp
        8.1
        ERX4294052
        77.7%
        5.8
        0.3%
        81.8%
        34%
        70 bp
        7.5
        ERX5228512
        81.0%
        10.9
        0.9%
        88.3%
        35%
        50 bp
        13.4
        ERX5228513
        80.2%
        9.3
        0.9%
        87.8%
        34%
        50 bp
        11.6
        ERX5228514
        81.8%
        12.0
        0.9%
        88.4%
        35%
        50 bp
        14.7
        ERX5228515
        79.2%
        9.6
        0.9%
        88.2%
        34%
        50 bp
        12.1
        ERX5228516
        81.2%
        7.6
        0.9%
        87.0%
        35%
        50 bp
        9.3
        ERX5228517
        82.4%
        11.1
        0.9%
        88.8%
        35%
        50 bp
        13.5
        Metab_1
        68.7%
        5.7
        96.3%
        8.0
        1.2%
        81.8%
        37%
        50 bp
        8.3
        Metab_10
        75.7%
        4.7
        96.6%
        6.0
        1.2%
        79.8%
        36%
        51 bp
        6.2
        Metab_11
        60.7%
        3.1
        95.8%
        4.8
        0.8%
        78.5%
        39%
        50 bp
        5.0
        Metab_12
        73.4%
        4.7
        96.8%
        6.2
        0.8%
        80.5%
        37%
        51 bp
        6.4
        Metab_13
        74.1%
        4.8
        96.3%
        6.2
        0.8%
        79.4%
        36%
        50 bp
        6.5
        Metab_14
        70.1%
        4.2
        96.0%
        5.8
        1.2%
        79.1%
        37%
        50 bp
        6.1
        Metab_15
        61.2%
        4.2
        96.6%
        6.6
        0.8%
        83.5%
        40%
        51 bp
        6.9
        Metab_16
        60.2%
        3.8
        96.8%
        6.1
        0.8%
        82.1%
        40%
        51 bp
        6.3
        Metab_17
        64.4%
        3.6
        96.1%
        5.4
        0.8%
        78.3%
        38%
        50 bp
        5.6
        Metab_18
        61.2%
        2.8
        95.9%
        4.4
        0.8%
        79.0%
        39%
        51 bp
        4.6
        Metab_19
        67.2%
        4.5
        96.8%
        6.6
        1.2%
        80.0%
        38%
        50 bp
        6.8
        Metab_2
        54.9%
        2.9
        96.1%
        5.0
        0.8%
        79.6%
        40%
        50 bp
        5.2
        Metab_20
        44.7%
        3.2
        96.6%
        6.8
        0.8%
        83.6%
        42%
        50 bp
        7.1
        Metab_3
        66.2%
        4.3
        96.6%
        6.2
        1.2%
        80.0%
        38%
        50 bp
        6.4
        Metab_4
        70.6%
        3.5
        95.8%
        4.8
        0.8%
        77.9%
        38%
        51 bp
        5.0
        Metab_5
        78.2%
        4.2
        96.8%
        5.2
        0.8%
        76.7%
        36%
        50 bp
        5.4
        Metab_6
        77.9%
        4.3
        96.5%
        5.3
        0.8%
        78.6%
        36%
        51 bp
        5.5
        Metab_7
        61.6%
        4.5
        97.0%
        7.1
        0.8%
        83.6%
        40%
        51 bp
        7.3
        Metab_8
        66.2%
        4.4
        96.5%
        6.5
        0.8%
        79.2%
        38%
        50 bp
        6.7
        Metab_9
        68.5%
        4.6
        96.5%
        6.4
        0.8%
        79.7%
        37%
        50 bp
        6.7
        Mia_0
        82.9%
        4.5
        98.2%
        5.3
        0.8%
        77.0%
        36%
        74 bp
        5.4
        Mia_1
        83.6%
        4.9
        98.3%
        5.8
        0.7%
        78.8%
        37%
        74 bp
        5.9
        Mia_2
        83.2%
        6.8
        98.4%
        8.1
        1.1%
        81.5%
        34%
        39 bp
        8.2
        Mia_3
        82.5%
        7.0
        98.1%
        8.3
        1.1%
        81.2%
        34%
        39 bp
        8.4
        Mia_4
        82.9%
        7.5
        97.9%
        8.8
        1.1%
        82.9%
        35%
        40 bp
        9.0
        Mia_5
        83.2%
        6.3
        98.0%
        7.5
        1.1%
        82.4%
        35%
        40 bp
        7.6
        Mia_6
        83.8%
        5.8
        98.1%
        6.8
        1.8%
        80.8%
        35%
        39 bp
        6.9
        Muc_1
        82.4%
        3.0
        1.5%
        68.8%
        37%
        40 bp
        3.6
        Muc_10
        87.9%
        2.6
        1.3%
        66.7%
        37%
        40 bp
        3.0
        Muc_11
        86.3%
        2.6
        1.3%
        66.9%
        37%
        40 bp
        3.0
        Muc_12
        87.0%
        2.5
        1.2%
        66.2%
        37%
        40 bp
        2.9
        Muc_13
        63.1%
        1.7
        2.9%
        67.1%
        39%
        40 bp
        2.6
        Muc_14
        63.5%
        2.0
        2.1%
        70.3%
        39%
        40 bp
        3.1
        Muc_15
        57.6%
        1.5
        3.4%
        66.2%
        40%
        40 bp
        2.6
        Muc_16
        61.4%
        1.5
        4.4%
        62.5%
        39%
        40 bp
        2.5
        Muc_17
        69.0%
        2.2
        1.7%
        65.5%
        38%
        40 bp
        3.2
        Muc_18
        68.6%
        2.8
        1.5%
        70.1%
        38%
        40 bp
        4.1
        Muc_19
        64.1%
        2.0
        1.4%
        71.1%
        39%
        40 bp
        3.1
        Muc_2
        81.8%
        2.3
        1.3%
        67.4%
        36%
        40 bp
        2.9
        Muc_20
        72.0%
        2.1
        1.6%
        68.7%
        38%
        40 bp
        3.0
        Muc_21
        59.6%
        2.2
        1.6%
        74.1%
        40%
        40 bp
        3.7
        Muc_22
        71.6%
        2.1
        1.6%
        68.8%
        38%
        40 bp
        2.9
        Muc_23
        67.3%
        1.9
        1.6%
        69.7%
        39%
        40 bp
        2.9
        Muc_24
        66.3%
        2.0
        1.8%
        70.0%
        39%
        40 bp
        3.1
        Muc_3
        82.0%
        2.2
        1.3%
        65.6%
        37%
        40 bp
        2.6
        Muc_4
        82.2%
        2.5
        1.4%
        66.5%
        37%
        40 bp
        3.0
        Muc_5
        86.0%
        2.5
        1.3%
        67.5%
        36%
        40 bp
        2.9
        Muc_6
        81.1%
        2.4
        1.2%
        68.4%
        37%
        40 bp
        2.9
        Muc_7
        78.1%
        2.0
        1.2%
        67.6%
        38%
        40 bp
        2.6
        Muc_8
        86.1%
        2.6
        1.2%
        69.2%
        36%
        40 bp
        3.0
        Muc_9
        81.1%
        2.1
        1.4%
        65.9%
        37%
        40 bp
        2.6
        SG_1
        77.2%
        9.1
        92.6%
        10.9
        0.9%
        71.4%
        34%
        50 bp
        11.8
        SG_2
        80.2%
        8.6
        93.0%
        10.0
        0.9%
        72.6%
        34%
        50 bp
        10.7
        SG_3
        74.8%
        6.9
        92.0%
        8.5
        0.9%
        67.3%
        35%
        50 bp
        9.2
        SG_4
        31.4%
        3.0
        92.2%
        8.9
        1.4%
        88.5%
        45%
        50 bp
        9.6
        SG_5
        76.3%
        9.5
        93.0%
        11.6
        0.9%
        73.1%
        34%
        50 bp
        12.5
        SG_6
        73.4%
        7.9
        93.0%
        10.0
        0.9%
        73.4%
        36%
        50 bp
        10.8
        SG_7
        76.8%
        6.8
        92.7%
        8.2
        1.3%
        81.2%
        36%
        51 bp
        8.9
        SG_8
        77.3%
        8.0
        92.4%
        9.5
        0.9%
        82.1%
        36%
        51 bp
        10.3
        SRX1357231
        0.0%
        0.0
        12.4%
        87.2%
        50%
        46 bp
        58.0
        SRX1357232
        0.0%
        0.0
        19.0%
        88.2%
        52%
        45 bp
        45.3
        SRX1357235
        0.1%
        0.0
        10.5%
        92.4%
        52%
        46 bp
        41.5
        SRX1357236
        0.1%
        0.0
        17.1%
        89.2%
        51%
        43 bp
        50.8
        SRX1357239
        0.0%
        0.0
        13.5%
        75.4%
        50%
        45 bp
        25.2
        SRX1357240
        0.2%
        0.1
        10.7%
        74.8%
        50%
        46 bp
        38.7
        SRX1357243
        0.3%
        0.1
        8.2%
        74.3%
        48%
        47 bp
        40.7
        SRX1357244
        0.0%
        0.0
        14.6%
        75.8%
        48%
        44 bp
        46.4
        SRX1549383
        0.2%
        0.0
        3.7%
        33.2%
        37%
        121 bp
        4.4
        SRX1549384
        23.1%
        0.8
        5.1%
        28.2%
        37%
        125 bp
        3.4
        SRX1983453
        0.8%
        0.0
        54.3%
        85.5%
        49%
        42 bp
        4.8
        SRX2629499
        0.1%
        0.0
        7.7%
        83.9%
        49%
        94 bp
        46.5
        SRX2629500
        0.0%
        0.0
        3.7%
        63.1%
        47%
        96 bp
        46.4
        SRX2722002
        73.2%
        2.4
        0.6%
        77.4%
        34%
        99 bp
        3.2
        SRX2722003
        72.5%
        2.6
        0.6%
        79.9%
        35%
        99 bp
        3.5
        SRX2722004
        67.6%
        2.5
        0.6%
        82.7%
        35%
        100 bp
        3.7
        SRX2722005
        76.5%
        3.0
        1.3%
        80.1%
        34%
        100 bp
        3.9
        SRX2722006
        77.5%
        3.3
        0.6%
        77.5%
        34%
        99 bp
        4.3
        SRX2722007
        77.8%
        2.8
        1.4%
        78.6%
        34%
        100 bp
        3.6
        SRX2722008
        77.3%
        2.6
        0.6%
        77.7%
        34%
        100 bp
        3.3
        SRX2722009
        77.0%
        2.8
        1.4%
        78.4%
        34%
        100 bp
        3.7
        SRX2722010
        79.2%
        3.0
        0.6%
        78.7%
        35%
        100 bp
        3.8
        SRX2722011
        76.9%
        3.0
        0.6%
        76.2%
        34%
        99 bp
        3.9
        SRX2722012
        77.9%
        3.3
        1.5%
        80.8%
        35%
        100 bp
        4.3
        SRX2722013
        82.9%
        3.7
        0.5%
        75.8%
        34%
        99 bp
        4.5
        SRX2722014
        84.1%
        3.1
        0.5%
        77.6%
        35%
        100 bp
        3.7
        SRX2722015
        83.2%
        2.8
        1.4%
        72.5%
        34%
        99 bp
        3.4
        SRX2722016
        82.2%
        3.0
        1.5%
        73.8%
        34%
        99 bp
        3.6
        SRX2722017
        82.2%
        3.2
        1.5%
        77.0%
        35%
        100 bp
        3.9
        SRX2722018
        82.3%
        3.7
        0.5%
        79.3%
        35%
        100 bp
        4.5
        SRX3489448
        61.8%
        3.1
        0.4%
        81.8%
        39%
        75 bp
        5.1
        SRX3489449
        51.3%
        5.4
        0.3%
        81.1%
        40%
        75 bp
        10.6
        SRX3489450
        55.4%
        2.2
        1.2%
        76.2%
        39%
        74 bp
        4.1
        SRX3489451
        62.8%
        2.0
        0.4%
        79.1%
        39%
        75 bp
        3.2
        SRX3489452
        54.6%
        2.4
        0.2%
        81.6%
        41%
        75 bp
        4.4
        SRX3489453
        44.5%
        2.1
        0.3%
        84.4%
        42%
        75 bp
        4.7
        SRX4065827
        82.6%
        5.2
        0.5%
        82.4%
        35%
        99 bp
        6.3
        SRX4065829
        78.9%
        4.3
        0.5%
        79.3%
        36%
        99 bp
        5.5
        SRX4065834
        80.4%
        4.1
        0.5%
        78.6%
        35%
        99 bp
        5.1
        SRX4065836
        81.9%
        5.0
        0.5%
        81.7%
        35%
        99 bp
        6.1
        SRX4065848
        82.7%
        4.8
        0.9%
        83.1%
        35%
        99 bp
        5.8
        SRX4913542
        27.5%
        1.3
        1.5%
        76.6%
        42%
        175 bp
        4.7
        SRX4913543
        44.5%
        1.8
        1.7%
        68.8%
        37%
        147 bp
        4.1
        SRX4913544
        0.0%
        0.0
        1.9%
        23.9%
        42%
        140 bp
        0.0
        SRX5014557
        80.1%
        2.7
        1.5%
        70.2%
        35%
        98 bp
        3.3
        SRX5014562
        68.5%
        4.9
        0.5%
        78.2%
        37%
        100 bp
        7.2
        SRX5014564
        84.2%
        5.8
        0.5%
        77.1%
        34%
        100 bp
        6.9
        SRX5014568
        83.2%
        6.4
        0.5%
        78.1%
        34%
        100 bp
        7.8
        SRX5014569
        76.5%
        2.1
        0.6%
        65.5%
        35%
        98 bp
        2.7
        SRX5014570
        56.4%
        4.2
        0.5%
        83.1%
        41%
        100 bp
        7.5
        SRX5014574
        80.9%
        2.9
        0.5%
        76.3%
        35%
        99 bp
        3.5
        SRX5014577
        79.0%
        2.4
        0.5%
        68.3%
        35%
        98 bp
        3.0
        SRX5014579
        81.1%
        2.9
        1.5%
        73.5%
        35%
        98 bp
        3.6
        SRX5014581
        79.9%
        6.4
        0.5%
        77.3%
        34%
        100 bp
        8.0
        SRX5014583
        83.8%
        7.0
        0.9%
        81.7%
        34%
        100 bp
        8.3
        SRX5014587
        81.1%
        5.9
        1.0%
        81.2%
        34%
        100 bp
        7.3
        SRX5014588
        82.0%
        5.8
        0.5%
        78.0%
        34%
        100 bp
        7.0
        SRX502154
        9.0%
        0.4
        19.3%
        59.1%
        48%
        123 bp
        4.4
        SRX502155
        17.4%
        0.6
        17.7%
        63.8%
        46%
        126 bp
        3.7
        SRX502158
        38.5%
        1.0
        13.4%
        59.5%
        41%
        131 bp
        2.6
        SRX5233212
        10.5%
        0.3
        4.4%
        59.3%
        47%
        49 bp
        2.5
        SRX5233213
        11.5%
        0.4
        2.0%
        71.0%
        48%
        50 bp
        3.4
        SRX5233214
        12.6%
        0.3
        0.8%
        82.9%
        48%
        50 bp
        2.0
        SRX5233215
        16.1%
        0.4
        0.8%
        82.7%
        47%
        50 bp
        2.6
        SRX5233216
        16.4%
        0.3
        0.8%
        82.4%
        47%
        50 bp
        1.7
        SRX5233217
        0.1%
        0.0
        1.1%
        81.4%
        49%
        50 bp
        3.5
        SRX5299657
        72.2%
        17.0
        5.0%
        91.0%
        34%
        120 bp
        23.6
        SRX5299658
        72.8%
        17.8
        4.6%
        91.2%
        34%
        120 bp
        24.5
        SRX5299659
        74.9%
        17.9
        4.6%
        91.9%
        34%
        120 bp
        23.9
        SRX5299660
        78.2%
        18.5
        4.5%
        91.4%
        35%
        120 bp
        23.6
        SRX5299661
        76.1%
        17.3
        5.5%
        91.3%
        35%
        120 bp
        22.8
        SRX5299662
        76.6%
        17.4
        5.3%
        91.4%
        35%
        120 bp
        22.8
        SRX5299663
        77.5%
        17.3
        5.5%
        90.7%
        35%
        120 bp
        22.3
        SRX5299664
        76.5%
        17.9
        4.5%
        91.0%
        35%
        120 bp
        23.4
        SRX5299665
        79.0%
        18.7
        5.6%
        91.7%
        35%
        120 bp
        23.7
        SRX5505131
        74.5%
        5.7
        1.0%
        79.4%
        34%
        99 bp
        7.7
        SRX5505132
        73.4%
        5.5
        0.4%
        78.6%
        33%
        99 bp
        7.5
        SRX5505133
        76.1%
        4.0
        0.4%
        80.5%
        35%
        99 bp
        5.3
        SRX5505134
        75.4%
        3.8
        0.4%
        76.4%
        34%
        99 bp
        5.0
        SRX5505135
        74.4%
        3.7
        0.4%
        75.8%
        34%
        99 bp
        4.9
        SRX5505136
        68.7%
        3.4
        0.4%
        78.0%
        34%
        99 bp
        4.9
        SRX5505137
        76.4%
        3.1
        0.4%
        80.5%
        35%
        99 bp
        4.1
        SRX5505138
        73.5%
        4.5
        0.4%
        84.1%
        35%
        99 bp
        6.2
        SRX5505139
        74.3%
        3.3
        0.4%
        81.3%
        35%
        99 bp
        4.4
        SRX5505140
        69.4%
        4.6
        1.0%
        85.0%
        34%
        99 bp
        6.7
        SRX5505141
        67.9%
        4.9
        0.4%
        79.0%
        35%
        99 bp
        7.2
        SRX5505142
        55.8%
        3.2
        0.5%
        84.2%
        38%
        99 bp
        5.7
        SRX5505143
        71.9%
        5.5
        0.4%
        78.3%
        34%
        99 bp
        7.7
        SRX5505144
        72.6%
        5.6
        0.4%
        78.6%
        34%
        99 bp
        7.7
        SRX5797722
        82.5%
        27.9
        1.7%
        91.9%
        34%
        98 bp
        33.7
        SRX5797723
        83.1%
        28.5
        3.4%
        92.5%
        35%
        99 bp
        34.3
        SRX5797724
        82.9%
        27.1
        3.4%
        92.4%
        35%
        99 bp
        32.7
        SRX5797725
        87.2%
        19.5
        1.7%
        89.6%
        34%
        98 bp
        22.4
        SRX5797726
        87.1%
        23.7
        3.5%
        90.9%
        35%
        98 bp
        27.2
        SRX5797727
        85.8%
        31.0
        3.4%
        92.1%
        34%
        98 bp
        36.1
        SRX5806783
        84.0%
        28.7
        1.3%
        92.0%
        34%
        99 bp
        34.1
        SRX5806784
        83.7%
        26.7
        2.1%
        92.4%
        35%
        99 bp
        31.8
        SRX5806785
        84.3%
        23.2
        1.3%
        91.6%
        35%
        99 bp
        27.5
        SRX5806786
        82.7%
        24.3
        2.2%
        90.6%
        34%
        99 bp
        29.4
        SRX5806787
        83.4%
        23.4
        1.3%
        91.7%
        35%
        99 bp
        28.0
        SRX5806788
        82.7%
        23.7
        1.3%
        92.0%
        35%
        99 bp
        28.7
        SRX6877996
        25.0%
        0.9
        64.4%
        64.4%
        43%
        40 bp
        3.5
        SRX6877997
        22.0%
        0.8
        85.6%
        66.2%
        44%
        41 bp
        3.6
        SRX6877998
        3.9%
        0.2
        71.5%
        80.2%
        50%
        30 bp
        5.2
        SRX6877999
        9.9%
        0.9
        57.7%
        83.5%
        46%
        39 bp
        8.6
        SRX6878000
        10.2%
        0.5
        67.0%
        80.6%
        46%
        34 bp
        4.5
        SRX6878001
        1.5%
        0.6
        48.8%
        92.8%
        45%
        46 bp
        42.8
        SRX6878002
        0.6%
        0.5
        63.2%
        93.8%
        48%
        37 bp
        78.5
        SRX6878003
        1.3%
        0.3
        80.8%
        86.6%
        50%
        33 bp
        21.4
        SRX6878004
        0.7%
        0.2
        69.3%
        95.6%
        50%
        33 bp
        29.1
        SRX6878005
        1.2%
        0.1
        78.7%
        73.0%
        50%
        32 bp
        7.3
        SRX6878006
        1.2%
        0.5
        63.6%
        92.1%
        49%
        33 bp
        37.1
        SRX6878007
        0.9%
        0.2
        71.3%
        77.5%
        49%
        34 bp
        24.7
        SRX6878008
        14.7%
        1.1
        65.8%
        82.9%
        49%
        38 bp
        7.2
        SRX6878009
        1.1%
        0.4
        78.2%
        67.9%
        48%
        34 bp
        33.0
        SRX6878010
        0.5%
        0.2
        66.6%
        84.8%
        49%
        37 bp
        45.1
        SRX6878011
        35.4%
        3.9
        56.8%
        63.7%
        43%
        42 bp
        10.9
        SRX6878012
        36.0%
        5.0
        55.9%
        63.6%
        42%
        41 bp
        13.8
        SRX6878013
        1.1%
        0.1
        70.9%
        74.5%
        54%
        36 bp
        8.1
        SRX6878014
        1.2%
        0.2
        71.0%
        78.5%
        54%
        35 bp
        16.2
        SRX6878015
        1.1%
        0.2
        69.9%
        79.3%
        54%
        35 bp
        19.2
        SRX6878016
        1.1%
        0.2
        69.0%
        80.1%
        54%
        35 bp
        18.1
        SRX6878017
        20.3%
        2.0
        55.3%
        73.2%
        44%
        40 bp
        9.6
        SRX6878018
        25.7%
        3.6
        47.5%
        71.5%
        42%
        46 bp
        14.0
        SRX6878019
        15.5%
        1.9
        54.4%
        85.1%
        46%
        39 bp
        12.0
        SRX6878020
        7.7%
        1.4
        63.8%
        75.2%
        50%
        36 bp
        17.6
        SRX6878021
        10.2%
        3.2
        57.4%
        73.8%
        49%
        38 bp
        31.2
        SRX6878022
        8.5%
        2.9
        55.0%
        76.6%
        50%
        38 bp
        33.9
        SRX6878023
        12.1%
        1.6
        51.6%
        87.7%
        46%
        41 bp
        13.6
        SRX6878024
        30.1%
        1.3
        76.7%
        68.5%
        44%
        41 bp
        4.3
        SRX6878025
        40.8%
        2.1
        82.5%
        66.5%
        43%
        40 bp
        5.1
        SRX6878026
        15.1%
        0.9
        67.3%
        82.7%
        48%
        37 bp
        6.0
        SRX6878027
        25.5%
        1.0
        77.5%
        87.1%
        47%
        33 bp
        3.9
        SRX6878028
        4.5%
        0.1
        76.2%
        76.3%
        48%
        29 bp
        2.9
        SRX7125364
        55.3%
        15.5
        0.8%
        84.2%
        41%
        74 bp
        28.1
        SRX7125365
        52.3%
        16.1
        0.8%
        84.9%
        42%
        74 bp
        30.9
        SRX7125366
        15.2%
        3.8
        1.0%
        68.8%
        47%
        74 bp
        25.3
        SRX7125367
        6.6%
        1.3
        0.9%
        71.8%
        51%
        74 bp
        20.1
        SRX7125368
        57.7%
        18.6
        0.9%
        85.2%
        40%
        74 bp
        32.2
        SRX7125369
        1.4%
        0.3
        0.9%
        81.6%
        54%
        74 bp
        18.6
        SRX7125370
        0.6%
        0.1
        1.2%
        70.7%
        52%
        73 bp
        21.7
        SRX7125371
        1.7%
        0.4
        1.0%
        67.2%
        51%
        74 bp
        21.4
        SRX7125372
        16.5%
        5.1
        0.9%
        69.0%
        49%
        74 bp
        30.9
        SRX7125373
        5.8%
        1.5
        1.1%
        56.7%
        49%
        74 bp
        26.5
        SRX7125374
        4.6%
        1.3
        1.3%
        60.0%
        48%
        73 bp
        28.7
        SRX7125375
        3.1%
        0.6
        1.1%
        65.8%
        50%
        73 bp
        20.9
        SRX8049163
        36.1%
        4.3
        1.5%
        81.7%
        39%
        73 bp
        11.8
        SRX8049164
        37.2%
        4.1
        1.7%
        81.6%
        39%
        73 bp
        11.0
        SRX8049165
        36.1%
        4.2
        1.6%
        81.5%
        38%
        73 bp
        11.6
        SRX8049166
        36.8%
        4.1
        1.7%
        81.7%
        39%
        73 bp
        11.1
        SRX8049167
        33.3%
        3.8
        2.4%
        81.3%
        39%
        73 bp
        11.4
        SRX8049168
        41.2%
        4.1
        1.7%
        79.8%
        37%
        73 bp
        10.0
        SRX8164260
        83.7%
        10.0
        1.6%
        86.6%
        36%
        40 bp
        12.0
        SRX8164261
        83.6%
        7.0
        1.6%
        83.1%
        35%
        39 bp
        8.3
        SRX8164262
        83.1%
        7.0
        1.7%
        82.7%
        35%
        39 bp
        8.4
        SRX8164263
        83.0%
        6.9
        1.1%
        83.0%
        36%
        39 bp
        8.3
        SRX8164264
        71.0%
        8.3
        1.6%
        85.8%
        38%
        39 bp
        11.6
        SRX8164265
        61.5%
        6.1
        1.1%
        86.0%
        39%
        40 bp
        9.9
        SRX8164266
        79.7%
        6.1
        1.1%
        83.1%
        36%
        40 bp
        7.7
        SRX8164267
        83.0%
        9.2
        1.1%
        86.3%
        35%
        40 bp
        11.1
        SRX8164268
        81.8%
        8.3
        1.7%
        89.1%
        36%
        40 bp
        10.2
        SRX8164269
        81.9%
        9.5
        1.7%
        85.3%
        36%
        40 bp
        11.6
        SRX8164270
        80.0%
        6.5
        1.9%
        82.6%
        36%
        39 bp
        8.1
        SRX8164271
        77.1%
        7.0
        1.6%
        83.4%
        37%
        39 bp
        9.0
        SRX8164272
        83.7%
        5.9
        1.6%
        82.6%
        35%
        40 bp
        7.0
        SRX8164273
        84.7%
        6.4
        1.7%
        83.3%
        35%
        40 bp
        7.6
        SRX8164274
        83.2%
        10.1
        1.1%
        85.8%
        36%
        40 bp
        12.1
        SRX8164275
        82.7%
        7.7
        1.1%
        84.0%
        35%
        40 bp
        9.3
        SRX8164276
        84.1%
        6.6
        1.1%
        82.9%
        35%
        40 bp
        7.9
        SRX8164277
        63.3%
        6.1
        1.6%
        85.1%
        39%
        39 bp
        9.7
        SRX8164278
        82.6%
        7.0
        1.1%
        83.4%
        35%
        40 bp
        8.5
        SRX8164279
        82.3%
        7.7
        1.7%
        83.5%
        35%
        39 bp
        9.3
        SRX8164280
        83.4%
        7.5
        1.1%
        82.9%
        36%
        39 bp
        9.0
        SRX8164281
        83.4%
        7.3
        1.1%
        82.9%
        35%
        39 bp
        8.8
        SRX8164282
        84.2%
        6.7
        1.7%
        81.9%
        35%
        39 bp
        8.0
        SRX8164283
        82.0%
        7.5
        1.1%
        83.8%
        35%
        40 bp
        9.2
        SRX8164284
        83.7%
        7.7
        1.1%
        82.5%
        34%
        39 bp
        9.2
        SRX8164285
        82.2%
        8.7
        1.7%
        84.3%
        35%
        40 bp
        10.5
        SRX8164286
        82.6%
        7.2
        1.7%
        82.7%
        35%
        39 bp
        8.7
        SRX8164287
        82.9%
        5.1
        1.1%
        80.4%
        35%
        39 bp
        6.1
        SRX8164288
        80.5%
        7.3
        1.6%
        83.9%
        36%
        39 bp
        9.1
        SRX8164289
        77.8%
        7.8
        1.6%
        85.0%
        37%
        39 bp
        10.0
        SRX8164290
        82.3%
        8.3
        1.1%
        84.7%
        36%
        40 bp
        10.0
        SRX8164291
        82.5%
        7.9
        1.1%
        84.5%
        36%
        40 bp
        9.6
        SRX8164292
        79.1%
        5.8
        1.1%
        83.3%
        37%
        40 bp
        7.4
        SRX8164293
        81.8%
        8.7
        1.6%
        85.2%
        36%
        40 bp
        10.6
        SRX8164294
        81.4%
        8.5
        1.7%
        83.5%
        36%
        39 bp
        10.4
        SRX8164295
        80.4%
        7.5
        1.6%
        85.1%
        37%
        40 bp
        9.3
        SRX8164296
        82.4%
        7.5
        1.7%
        82.5%
        33%
        39 bp
        9.1
        SRX8164297
        82.6%
        6.7
        1.1%
        81.5%
        34%
        40 bp
        8.1
        SRX8164298
        81.2%
        7.7
        1.1%
        83.8%
        34%
        40 bp
        9.5
        SRX8164299
        80.8%
        7.2
        1.8%
        83.7%
        34%
        40 bp
        9.0
        SRX8164300
        79.2%
        6.6
        1.1%
        80.6%
        36%
        39 bp
        8.3
        SRX8164301
        83.3%
        8.5
        1.1%
        83.9%
        35%
        40 bp
        10.2
        SRX8164302
        83.6%
        5.7
        1.7%
        81.5%
        35%
        39 bp
        6.9
        SRX8164303
        83.0%
        7.4
        1.7%
        84.0%
        35%
        40 bp
        8.9
        SRX8164304
        79.5%
        8.5
        1.7%
        84.9%
        35%
        40 bp
        10.7
        SRX8164305
        80.9%
        7.0
        1.1%
        82.8%
        36%
        39 bp
        8.7
        SRX8164306
        82.7%
        7.0
        1.7%
        82.5%
        35%
        39 bp
        8.5
        SRX8164307
        82.5%
        5.3
        1.1%
        80.1%
        35%
        39 bp
        6.4
        SRX8387559
        66.6%
        3.7
        0.6%
        59.8%
        34%
        99 bp
        5.6
        SRX8387560
        68.1%
        4.1
        0.5%
        79.7%
        34%
        99 bp
        6.1
        SRX8387561
        84.7%
        8.0
        1.1%
        82.5%
        35%
        40 bp
        9.4
        SRX8387562
        84.4%
        7.9
        1.8%
        83.4%
        35%
        40 bp
        9.4
        SRX8387563
        83.8%
        7.5
        1.1%
        82.1%
        35%
        40 bp
        9.0
        SRX8387564
        85.3%
        8.1
        1.8%
        82.3%
        35%
        39 bp
        9.5
        SRX8387565
        83.8%
        7.8
        1.1%
        82.5%
        35%
        40 bp
        9.3
        SRX8387566
        84.9%
        8.4
        1.8%
        83.3%
        35%
        40 bp
        9.9
        SRX8387567
        83.2%
        9.4
        1.1%
        83.6%
        34%
        39 bp
        11.2
        SRX8387568
        82.6%
        8.9
        1.9%
        83.2%
        34%
        39 bp
        10.8
        SRX8387571
        67.0%
        3.6
        0.5%
        61.1%
        34%
        99 bp
        5.3
        SRX8387574
        83.0%
        8.6
        1.6%
        85.7%
        35%
        40 bp
        10.3
        SRX8387575
        82.8%
        6.6
        1.6%
        81.6%
        36%
        39 bp
        8.0
        SRX8387576
        82.6%
        7.5
        1.1%
        84.9%
        35%
        40 bp
        9.1
        SRX8387577
        82.9%
        6.4
        1.1%
        80.2%
        36%
        39 bp
        7.7
        SRX8387582
        66.9%
        4.6
        1.1%
        80.2%
        34%
        99 bp
        6.8
        SRX8387589
        64.6%
        4.1
        0.5%
        58.5%
        35%
        99 bp
        6.4
        SRX8387590
        68.0%
        3.7
        1.1%
        77.0%
        34%
        99 bp
        5.5
        SRX8387591
        61.9%
        3.8
        1.1%
        60.5%
        33%
        99 bp
        6.2
        SRX8387592
        61.9%
        4.3
        1.1%
        62.7%
        33%
        99 bp
        6.9
        SRX8387593
        84.5%
        9.4
        1.8%
        82.9%
        34%
        39 bp
        11.1
        SRX8387594
        85.3%
        6.7
        1.1%
        80.8%
        35%
        39 bp
        7.8
        SRX8420202
        85.9%
        6.5
        1.1%
        84.4%
        36%
        40 bp
        7.6
        SRX8420203
        85.7%
        7.4
        1.0%
        84.9%
        36%
        40 bp
        8.7
        SRX8420204
        0.5%
        0.0
        1.6%
        84.7%
        35%
        39 bp
        9.4
        SRX8420205
        0.5%
        0.0
        1.0%
        86.2%
        36%
        40 bp
        9.2
        SRX8420206
        85.9%
        7.4
        1.7%
        83.8%
        35%
        39 bp
        8.6
        SRX8420207
        0.4%
        0.0
        1.6%
        85.9%
        36%
        40 bp
        9.0
        SRX8420208
        0.5%
        0.0
        1.7%
        84.9%
        35%
        39 bp
        9.5
        SRX8420209
        86.7%
        7.2
        1.0%
        85.3%
        36%
        40 bp
        8.3
        SRX9633794
        32.6%
        9.8
        0.5%
        93.4%
        39%
        122 bp
        30.0
        SRX9633795
        35.1%
        8.9
        0.2%
        94.5%
        39%
        127 bp
        25.4
        SRX9633796
        31.8%
        8.6
        1.0%
        89.9%
        40%
        127 bp
        27.1
        SRX9633797
        36.8%
        9.6
        0.7%
        95.0%
        39%
        135 bp
        26.1
        SRX9633798
        39.9%
        14.3
        0.3%
        91.9%
        39%
        121 bp
        35.8
        SRX9633799
        34.8%
        7.9
        1.0%
        88.1%
        40%
        128 bp
        22.8
        SRX9633800
        29.5%
        6.5
        2.0%
        95.2%
        41%
        131 bp
        22.1
        SRX9633801
        34.7%
        11.6
        0.4%
        91.0%
        40%
        126 bp
        33.4
        SRX9633802
        38.0%
        16.3
        0.3%
        91.4%
        40%
        126 bp
        43.0
        SRX9682649
        46.7%
        2.0
        17.8%
        69.9%
        53%
        69 bp
        4.2
        SRX9682654
        66.7%
        7.5
        0.6%
        87.0%
        39%
        74 bp
        11.3
        SRX9682659
        84.6%
        9.3
        0.9%
        80.2%
        35%
        75 bp
        11.0
        SRX9682664
        81.5%
        7.5
        0.9%
        80.9%
        35%
        75 bp
        9.2
        SRX9682669
        78.9%
        11.9
        0.6%
        87.2%
        39%
        75 bp
        15.1
        SRX9682674
        76.3%
        12.2
        0.9%
        85.5%
        36%
        75 bp
        16.0
        SRX9699053
        71.1%
        7.2
        1.0%
        70.3%
        33%
        74 bp
        10.1
        SRX9699054
        70.0%
        6.0
        1.1%
        67.3%
        34%
        74 bp
        8.6
        SRX9699055
        79.9%
        8.0
        0.9%
        70.8%
        34%
        74 bp
        10.0
        SRX9699056
        76.4%
        7.6
        0.9%
        67.7%
        34%
        74 bp
        9.9
        SRX973265
        17.2%
        2.4
        7.2%
        87.9%
        37%
        87 bp
        14.2
        SRX973266
        4.7%
        0.5
        5.7%
        95.7%
        42%
        89 bp
        11.4
        SRX973267
        10.5%
        1.2
        4.4%
        88.0%
        44%
        90 bp
        10.9
        SRX973268
        10.4%
        1.1
        4.2%
        87.9%
        45%
        90 bp
        10.3
        SRX9960951
        75.1%
        17.0
        18.5%
        73.8%
        33%
        74 bp
        22.6
        SRX9960952
        76.0%
        15.6
        18.1%
        74.5%
        32%
        74 bp
        20.5
        SRX9960953
        75.7%
        20.1
        15.8%
        74.6%
        34%
        73 bp
        26.6
        SRX9960954
        75.7%
        6.9
        25.2%
        71.8%
        33%
        73 bp
        9.1
        SRX9960955
        78.5%
        20.0
        2.3%
        64.8%
        33%
        73 bp
        25.4
        SRX9960956
        77.9%
        10.0
        6.4%
        71.6%
        33%
        73 bp
        12.9
        SRX9960957
        76.8%
        11.5
        7.9%
        72.4%
        33%
        74 bp
        14.9
        SRX9960958
        75.6%
        12.2
        9.5%
        72.6%
        33%
        74 bp
        16.1
        SRX9960959
        76.2%
        12.6
        23.5%
        74.5%
        33%
        73 bp
        16.6
        SRX9960960
        74.8%
        5.6
        30.4%
        70.3%
        33%
        73 bp
        7.4
        SRX9960961
        75.0%
        11.4
        24.7%
        72.5%
        33%
        73 bp
        15.3
        SRX9960962
        74.4%
        8.5
        25.2%
        73.3%
        32%
        73 bp
        11.4
        SRX9960963
        74.4%
        7.1
        26.7%
        72.9%
        32%
        73 bp
        9.5
        SRX9960964
        73.1%
        11.0
        26.9%
        73.5%
        33%
        74 bp
        15.1
        SRX9960965
        78.3%
        10.8
        24.5%
        71.6%
        33%
        73 bp
        13.8
        SRX9960966
        77.3%
        15.7
        19.3%
        73.5%
        33%
        73 bp
        20.4
        Vir_1
        66.2%
        3.0
        76.9%
        3.5
        0.6%
        83.4%
        34%
        151 bp
        4.6
        Vir_10
        66.7%
        2.8
        75.8%
        3.2
        0.4%
        26.2%
        36%
        150 bp
        4.3
        Vir_11
        71.6%
        2.6
        81.7%
        3.0
        0.4%
        20.7%
        36%
        150 bp
        3.7
        Vir_12
        70.4%
        3.2
        80.5%
        3.7
        0.4%
        81.1%
        35%
        150 bp
        4.6
        Vir_13
        70.6%
        3.0
        81.5%
        3.5
        0.5%
        77.7%
        35%
        150 bp
        4.3
        Vir_14
        68.8%
        2.9
        80.3%
        3.4
        0.5%
        20.5%
        36%
        150 bp
        4.3
        Vir_15
        67.1%
        3.5
        79.6%
        4.1
        0.5%
        79.2%
        34%
        150 bp
        5.2
        Vir_16
        65.9%
        3.1
        78.7%
        3.7
        0.7%
        19.0%
        36%
        150 bp
        4.7
        Vir_17
        70.3%
        3.2
        81.0%
        3.7
        0.6%
        20.4%
        36%
        150 bp
        4.5
        Vir_18
        69.8%
        2.7
        80.8%
        3.2
        0.6%
        18.5%
        36%
        150 bp
        3.9
        Vir_19
        63.5%
        2.0
        73.3%
        2.3
        0.6%
        77.0%
        34%
        151 bp
        3.2
        Vir_2
        62.0%
        2.8
        71.5%
        3.3
        0.6%
        56.3%
        36%
        150 bp
        4.5
        Vir_20
        67.3%
        2.7
        77.8%
        3.1
        0.4%
        79.6%
        34%
        151 bp
        4.0
        Vir_3
        69.4%
        3.1
        76.8%
        3.4
        0.4%
        81.6%
        34%
        151 bp
        4.5
        Vir_4
        76.2%
        2.5
        85.8%
        2.8
        0.4%
        20.0%
        36%
        150 bp
        3.2
        Vir_5
        71.0%
        2.6
        80.6%
        2.9
        0.7%
        20.1%
        36%
        150 bp
        3.6
        Vir_6
        69.2%
        2.5
        79.9%
        2.9
        0.5%
        18.8%
        36%
        150 bp
        3.7
        Vir_7
        70.0%
        2.7
        79.2%
        3.0
        0.7%
        76.9%
        35%
        150 bp
        3.8
        Vir_8
        69.9%
        2.9
        78.7%
        3.2
        0.5%
        19.7%
        36%
        150 bp
        4.1
        Vir_9
        65.8%
        2.6
        86.3%
        3.4
        0.6%
        78.6%
        37%
        151 bp
        3.9

        featureCounts

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Bowtie 1

        Bowtie 1 is an ultrafast, memory-efficient short read aligner.

        This plot shows the number of reads aligning to the reference in different ways.

        There are 3 possible types of alignment: * Aligned: Read has only one occurence in the reference genome. * Multimapped: Read has multiple occurence. * Not aligned: Read has no occurence.

        loading..

        RSeQC

        RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Trimmed Sequence Lengths

        This plot shows the number of reads with certain lengths of adapter trimmed.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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